Dr. Shaffer's research program involves the application of statistical and bioinformatics approaches to understand the genetic contributors to common complex human diseases. In particular, Dr. Shaffer is interested in heritability, linkage analysis, genetic association, epigenetics, and gene-by-environment interactions. His current research projects include studies of oral health, craniofacial phenotypes, and recovery from brain injury.
2008 | University of Pittsburgh, Pittsburgh, PA | Ph.D. in Human Genetics
2003 | The Pennsylvania State University, University Park, PA | B.S. in Biology
2008-2022 | HUGEN 2022 Human Population Genetics
offered each Fall semester
2020-present | HUGEN 2080 Statistical Genetics
offered biennially in the Spring semester
2022-present | HUGEN 2020 Population Genetics and Genetic Epidemiology
offered each Fall semester
Recent published works (1/2022 to 6/2024)
Niklas Fries, Simon Haworth, John R Shaffer, Anders Esberg, Kimon Divaris, Mary L Marazita, Ingegerd Johansson. A Polygenic Score Predicts Caries Experience in Elderly Swedish Adults. J Dent Res. (in press).
Emyli Peralta, Jacqueline M Burgette, Tayla J Tallman, Carly A Scala, Brette N Scala, Zelda T Dahl, Robert J Weyant, John R. Shaffer, Betsy Foxman, Daniel W McNeil, Mary L Marazita. Maternal Perceptions of Assisting Pre-school Aged Children with Toothbrushing. Journal of the American Dental Association. (in press)
Anthony M Musolf, Cristina M Justice, Zeynep Erdogan-Yildirim, Seppe Goovaerts, Araceli Cuellar, John R Shaffer, Mary L Marazita, Peter Claes, Seth M Weinberg, Jae Li, Craig Senders, Marike Zwienenberg, Emil Simeonov, Radka Kaneva, Tony Roscioli, Lorena Di Pietro, Marta Barba, Wanda Lattanzi, Michael L Cunningham, Paul A Romitti, Simeon A Boyadjiev. Whole genome sequencing identifies associations for nonsyndromic sagittal craniosynostosis with the intergenic region of BMP2 and noncoding RNA gene LINC01428. Scientific Reports 2024 Apr 12;14(1):8533.
Jaaved Mohammed, Neha Arora, Harold S. Matthews, Karissa Hansen, Maram Bader, John R. Shaffer, Seth M. Weinberg, Tomek Swigut, Peter Claes, Licia Selleri, Joanna Wysocka. A common cis-regulatory variant impacts normal-range and disease-associated human facial shape through regulation of PDKCC during chondrogenesis. Elife. 2024 Mar 14:13:e82564.
Morgan Byrd, Elyse Davis, Freida Blostein, Deesha Bhaumik, Katherine Neiswanger, John R. Shaffer, Daniel McNeil, Mary L. Marazita, Betsy Foxman. Risk of postpartum dental caries: survival analysis of Black/African American and White women in Appalachia. Womens Health Rep (New Rochelle) 2024 Feb 15;5(1):108-119.
Seppe Goovaerts, Hanne Hoskens, Ryan J Eller, Anthony M Musolf, Christina M Justice, Meng Yuan, Sahin Naqvi, Noah C Herrick, Myoung Keun Lee, Dirk Vandermeulen, Heather L Szabo-Rogers, Paul A Romitti, Simeon A Boyadjiev, Mary L Marazita, John R Shaffer, Mark D Shriver, Joanna Wysocka, Susan Walsh, Seth M Weinberg, Peter Claes. Multiethnic GWAS reveals the complex genetics behind human cranial vault shape. Nature Communications 2023 Nov 16;14(1):7436.
Meng Yuan, Seppe Goovaerts, Hanne Hoskens, Stephen Richmond, Susan Walsh, Mark D. Shriver, John R. Shaffer, Mary L. Marazita, Seth M. Weinberg, Hilde Peeters, and Peter Claes. Data-driven trait heritability-based extraction of human facial phenotypes. Proceedings of the Institute of Electrical and Electronics Engineers International Conference on Bioinformatics and Biomedicine (in press).
Jamie L. Perry, Myoung Keun Lee, Neda Tahmasebifard, Imani R. Gilbert, Taylor D. Snodgrass, John R. Shaffer, Eshan Pua Schleif, Seth M. Weinberg. Sex differences in velopharyngeal anatomy of 9–10-year-old children. Journal of Speech, Language, and Hearing Research 2023 Dec 11;66(12):4828-4837.
Tianyu Zou (mentee), Katherine Neiswanger, Eleanor Feingold, Betsy Foxman, Daniel McNeil, Mary L. Marazita, John R. Shaffer (corresponding author). Potential risk factors and genetic variants associated with dental caries incidence in Appalachia using genome-wide survival analysis. International Journal of Molecular Epidemiology and Genetics 2023;14(2):19-33.
Freida Blostein, Tianyu Zou (mentee), Deesha Bhaumik, Elizabeth Salzman, Kelly Bakulski, John R. Shaffer, Mary Marazita, Betsy Foxman. Bacterial community modifies host genetics effect on early childhood caries. Journal of Dental Research 2023 Sep;102(10):1098-1105.
Tianyu Zou (mentee), Betsy Foxman, Daniel W. McNeil, Seth M. Weinberg, Mary L. Marazita, John R. Shaffer (corresponding author). Genome-Wide Analysis of Dental Caries Variability Reveals Genotype-by-Environment Interactions. Genes 2023 Mar 17;14(3):736.
Franziska Wilke, Noah Herrick, Harold Matthews, Hanne Hoskens, Sylvia Singh, John R. Shaffer, Seth M. Weinberg, Mark D. Shriver, Peter Claes, Susan Walsh. Exploring Regional Aspects of 3D Facial Variation in a European Population. Scientific Reports. 2023 Mar 6;13(1):3708.
Harold S Matthews; Soha Mahdi; Anthony J Penington; Mary L Marazita; John R Shaffer; Susan Walsh; Mark D Shriver; Peter Claes; Seth M Weinberg. Using Data-Driven Phenotyping to Investigate the Impact of Sex on 3D Human Facial Surface Morphology. Journal of Anatomy. Journal of Anatomy 2023 Aug; 243(2): 274– 283.
Ekaterina Orlova (mentee), Tom Dudding, Jonathan M. Chernus, Rasha N. Alotaibi, Simon Haworth, Richard J. Crout, Myoung Keun Lee, Nandita Mukhopadhyay, Eleanor Feingold, Steven M. Levy, Daniel W. McNeil, Betsy Foxman, Robert J. Weyant, Nicholas J. Timpson, Mary L. Marazita, John R. Shaffer (corresponding author). Association of early childhood caries with bitter taste receptors: a meta-analysis of genome-wide association studies and transcriptome-wide association study. Genes 2023, 14(1), 59.
Deesha Bhaumik, Casey D. Wright, Teresa A. Marshall, Katherine Neiswanger, Daniel W. McNeil, Andrew D. Jones, John R. Shaffer, Mary L. Marazita, Betsy Foxman. Food insecurity and consumption of cariogenic foods in mothers and their two-year-old children in Appalachia. Journal of Public Health Dentistry. Journal of Public Health Dentistry 2023;83:127–135.
Tiwari T, Randall CL, Rai N, Carey C, Shaffer JR, Finlayson T, Kaste LM, Daviglus ML, Laniado N, Singer R. Acculturation and Dental Care-Related Anxiety: An Assessment from the Hispanic Community Health Study / Study of Latinos. Journal of Immigrant and Minority Health. 2023 Jun;25(3):616-623.
Betsy Foxman, Elyse Davis, Katherine Neiswanger, Daniel W McNeil, John R Shaffer, Mary L. Marazita. Maternal factors and risk of early childhood caries: A prospective cohort study. Community Dent Oral Epidemiol. 2023; 51(5): 953-965.
Erica C. Jansen, Wentong Zhao, Andrew D. Jones, Teresa A. Marshall, Katherine Neiswanger, John R. Shaffer, Daniel W. McNeil, Mary L. Marazita, Betsy Foxman. Early childhood diet in relation to toddler nighttime sleep duration trajectories. Nutrients 2022 Jul 26;14(15):3059.
Myoung Keun Lee, Zelda T. Dahl, Joel Anderton, Jennifer L. Maurer, Mary L. Marazita, John R. Shaffer, Seth M. Weinberg. Bent Pinkies: Quantifying Fifth Finger Clinodactyly in a Sample of U.S. Adults. PLOS One 2022 Jul 20;17(7):e0271734.
Kimon Divaris, Simon Haworth, John R. Shaffer, Vuokko Anttonen, James D. Beck, Yasushi Furuichi, Birte Holtfreter, Daniel Jönsson, Thomas Kocher, Steven M. Levy, Patrik K.E. Magnusson, Daniel W. McNeil, Karl Michaëlsson, Kari E. North, Ulla Palotie, Panos N. Papapanou, Pirkko J. Pussinen, David Porteous, Kadri Reis, Aino Salminen, Arne S. Schaefer, Takeaki Sudo, Yi-Qian Sun, Anna Liisa Suominen, Toru Tamahara, Seth M. Weinberg, Pernilla Lundberg, Mary L. Marazita, Ingegerd Johansson. Phenotype Harmonization in the GLIDE2 Oral Health Genomics Consortium Journal of Dental Research 2022 Oct;101(11):1408-1416.
Kalo Sokoto, Lisa Platt, Linda Alexander, Betsy Foxman, John R. Shaffer, Mary L. Marazita, Daniel W. McNeil. Racism, Dental Care-Related Fear/Anxiety, and Oral Healthcare Utilization among Black/African American Women in Appalachia. Journal of Public Health Dentistry. 2022 Mar;82 Suppl 1:28-35.
Yuqiao Zhou (mentee), Daniel W. McNeil, Simon Haworth, Tom Dudding, Jonathan M. Chernus, Chenxing Liu (mentee), Dongjing Liu (mentee), Casey D. Wright, Jamey Brumbaugh, Cameron L. Randall, Robert J. Weyant, Richard J. Crout, Betsy Foxman, Steven Reis, Nicolas J. Timpson, Mary L. Marazita, John R. Shaffer (corresponding author). Genome-wide scan of dental fear and anxiety nominates novel genes. Journal of Dental Research 2022 Nov;101(12):1526-1536.
Nandita Mukhopadhyay, Eleanor Feingold, Lina Moreno-Uribe, George Wehby, Luz Consuelo Valencia-Ramirez, Claudia P. Restrepo Muñeton, Carmencita Padilla, Frederic Deleyiannis, Kaare Christensen, Fernando A. Poletta, Ieda M Orioli, Jacqueline T. Hecht, Carmen J. Buxó, Azeez Butali, Wasiu L. Adeyemo, Alexandre R. Vieira, John R. Shaffer, Jeffrey C. Murray, Seth M. Weinberg, Elizabeth J. Leslie, Mary L. Marazita. Genome-wide association study of non-syndromic orofacial clefts in a multiethnic sample of families and controls identifies novel regions. Genetic Epidemiology. 2022 Apr;46(3-4):182-198.
Jenna Carlson, John R. Shaffer, Fred Deleyiannis, Jacqueline T. Hecht, George L. Wehby, Kaare Christensen, Eleanor Feingold, Seth M. Weinberg, Mary L. Marazita, Elizabeth Leslie. Genome-wide interaction study implicates VGLL2 and alcohol exposure and PRL and smoking in orofacial cleft risk. Frontiers in Cell and Developmental Biology. 2022 Feb 10;10:621261
Dongjing Liu (mentee), Benjamin E. Zusman, John R. Shaffer, Yunqi Li (mentee), Annie I. Arockiaraj (mentee), Shuwei Liu, Daniel E. Weeks, Shashvat M. Desai, Patrick M. Kochanek, Ava M. Puccio, David O. Okonkwo, Yvette P. Conley, Ruchira M. Jha. Decreased DNA methylation of RGMA is associated with intracranial hypertension after severe traumatic brain injury: an exploratory epigenome-wide association study. Neurocricial Care. 2022 Aug;37(1):26-37.
